Breast cancers are among the most frequently occurring tumors in women worldwide, and the clinical course and disease free survival times for patients with breast cancers are extremely heterogeneous. Accordingly, intensive efforts have been made over the past decades to develop biological markers that allow for precise disease staging and prognostication. Such markers include tumor size, grade and stage, lymph node and hormone receptor status, expression of growth factor receptors, DNA content, S-phase fraction and proliferative activity, and, more recently, specific gene expression signatures that suggest a poor prognosis. Genomic instability also is a common trait of breast cancers and impacts on prognosis. Genomic instability is the tendency of the cells of a tissue to exhibit diversity in the amount of nuclear DNA present, principally due to chromosomal rearrangement and duplication. This parameter of cancer tissue typically is assessed on the basis of cytometric measurements of nuclear DNA content, and is not directly accounted for in most established prognostic tests. Thus, there remains a need for new methods and compositions that can be used to prognosticate the clinical course and survival times of breast cancer patients, especially those that account for genomic instability.